Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

Augusto Berrocal, Nicholas Lammers, Hernan Garcia, Michael Eisen: Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene, bioRxiv, 335901 (2018). doi:


We used the MS2 system to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high spatiotemporal resolution spanning nuclear cycle 14. We observe extensive transcriptional bursting across the anteroposterior axis, initially in broad domains that are refined over the course of approximately 15 minutes to form the iconic seven striped expression pattern. We developed a rigorous quantitative framework for analyzing and visualizing these data, that allows us to simultaneously infer the high-resolution temporal dynamics of the transcriptional state of roughly 3,000 nuclei, and characterize how the bursting process varies over time and space. We show that despite being created by the largely independent activity of five discrete enhancers, the seven eve stripes are sculpted by the same basic kinetic phenomena - a low burst frequency outside of stripes, and a high burst frequency inside the stripe that increases over time to sharpen the contrast between stripe and interstripe regions.